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RNAseq of brain and muscle from Nadk2 and Pla2g6 mutant mice at early and late phenotypic time points

ABSTRACT: RNAseq of brain and muscle from Nadk2 and Pla2g6 mutant mice at early and late phenotypic time points

PROVIDER: PRJNA779476 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16914300.fastq.gz	Fastqsanger.gz
	SRR16914301.fastq.gz	Fastqsanger.gz
	SRR16914302.fastq.gz	Fastqsanger.gz
	SRR16914303.fastq.gz	Fastqsanger.gz
	SRR16914304.fastq.gz	Fastqsanger.gz

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Project description:It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions. While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20°C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce.

Dataset Information

RNAseq of brain and muscle from Nadk2 and Pla2g6 mutant mice at early and late phenotypic time points

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